Wetware advances: Biological logic gate built by splitting viral gene

Scientists make a genetic AND gate with the help of a T7 bacteriophage.

In recent years, researchers in the messy world of biology have been able to build systems that function like the clean, binary switches on computer chips—and we've covered a number of reports in this area. Unfortunately, most of these share a significant limitation: they rely on proteins from bacteria that act as switches to turn genes on and off under specific conditions. We know about only a limited number of these genetic switches, which may set a severe limit on the number of logical operations we can string together inside a cell.

A paper in this week's PNAS describes a system that may allow us to get around this limitation. The new method takes a protein from a virus that infects bacteria and cuts it in two, making a pair of genes (A and B) that each produce part of the mature protein. The two parts then act as a biological version of an AND logic gate, with output (in the form of protein activity) present only when both A and B interact. When either or both A and B are missing, the output is off.

In biological terms, the inputs usually involve a simple molecule that can be sensed by proteins inside a bacteria. This paper, for example, used two kinds of sugars (arabinose and lactose). When the sugars are present, they attach to proteins inside the cell, activating genes that are controlled by those proteins. To make an AND gate, you need to design a bit of biology that can respond to both of these signals—it should be active only when both a gene regulated by arabinose and a gene regulated by lactose are each active.

This has been done in a variety of ways in the past, but the authors of the new paper (both faculty at Rice University) come up with a clever scheme for doing so. It's clever in part because it's so remarkably simple.

The uses of a T7 bacteriophage

The new work relies on a gene from a virus called the T7 bacteriophage that infects bacteria. Instead of relying on host proteins to ensure that its genes are turned into RNA (and thus into proteins), T7 carries its own gene for a protein that transcribes DNA into RNA. This gene, called (wait for it) T7 RNA polymerase, recognizes DNA sequences on the virus, sticks to them, and then starts copying the DNA nearby into RNA. If you move the sequences it recognizes somewhere else—into the bacterial genome, onto a construct you supply—it will start copying there instead.

T7 RNA polymerase therefore makes a good output. When it's active, you can use it to turn on a variety of genes, thus coordinating a significant response to your logic. But how do you get T7 RNA polymerase to respond to the two different inputs required for an AND gate? You break it in two.

Scientists who were studying T7 RNA polymerase had found that, during purification, it would sometimes get cut into two different pieces, one about four times the size of the other. Either of the parts on its own is inactive, but if you put them together they stick, and the resulting aggregate is active (that is, it would bind to the appropriate DNA sequences and start making RNA, albeit at a slightly slower rate than the intact protein).

It turns out this also works if the two parts are encoded by completely separate genes. You can encode the larger T7 RNA polymerase fragment in a gene that responds to arabinose and the smaller fragment in a gene that responds to lactose. A functional T7 RNA polymerase will only be present when both sugars are present, so you've made your biological AND gate.

By putting a fluorescent protein under the control of T7 RNA polymerase, the authors were able to show that this worked as expected. The cells glowed green only when both sugars were added.

That on its own is pretty good, although not so much better than some previous work in the field. The great part of this system is its flexibility. Because T7 RNA polymerase has been studied extensively, researchers have identified a variety of mutations that alter the protein's ability to bond to specific DNA sequences. A single change in the right location can thus switch T7 RNA polymerase from sticking to (for example) a sequence that includes GACG to one that includes the sequence GCAT. Other changes in the T7 RNA polymerase can alter the sequence it recognizes even further.

Instead of relying on different proteins for every logical operation you need to do (which will quickly exhaust your supply of tractable proteins), you can now build up logic using different forms of T7 RNA polymerase, each recognizing a somewhat different sequence. This doesn't necessarily help with alternate logic operations, like NOT, but having a larger array of potential tools can only make designing biological circuitry easier.

Nice picture, but I find it interesting how we're trying to shoehorn one methodology into another instead of developing the strengths of what's already there. There's a reason biology works the way it does and our brains clearly show there's merit to it's madness.

Nice picture, but I find it interesting how we're trying to shoehorn one methodology into another instead of developing the strengths of what's already there. There's a reason biology works the way it does and our brains clearly show there's merit to it's madness.

I was thinking along this same line, though I imagine it would be easier for programmer, or a computer, or whomever, to encode and decode the instructions, since we are already (generally) familiar with the logic instructions we've created for transistorized logic gates.

What's the use of being able to do this? Other than to say "that's cool!"

One approach to 'synthetic biology,' is to start with a bacteria whose genome has been pared down to the minimum essentials for reproduction, and then add in features. Being able to replicate all of the logic operations might aid the creation of a human-writable "biological programming language," that isn't just trial and error.

In natural cells, activating a particular gene or set of genes can be the result of many, many proteins interacting with each other (often interacting in interesting ways with the structure of DNA itself). This complexity can make it hard to co-opt certain cell mechanisms for our own engineered organisms, since a particular function might be subtly influenced by features of seemingly unrelated proteins.

Imagine being able to look at this library: http://partsregistry.org/Main_Page and being able to piece together a bacteria that takes a few inputs (just add in this receptor gene for detecting shigella toxin!) and link it via logic operators to some output (produce green fluorescent protein). Feed it to cows, and now you just look at their poop to see which is contaminated.

What's the use of being able to do this? Other than to say "that's cool!"

A working wetware AND gate would be the first step to creating an artificial neuron. Properly setting up a cluster of these neurons and designing a program to run on the cluster would be the first step to a biological computer.

Considering that the human brain is basically an advanced form of wetware--not to mention the most powerful processing device still known to man, capable of not only advanced calculations but imaginative thought processes, meaning the ability to design its own complex models and draw conclusions logically (most of the time) advances in wetware are far more than just "cool". Advances in merging biological computing with current technological--hardware--designs could be range from the next step in our evolutionary process, curing memory damaging diseases like Alzheimers or creating the first true artificial intelligence.

What's the use of being able to do this? Other than to say "that's cool!"

A working wetware AND gate would be the first step to creating an artificial neuron. Properly setting up a cluster of these neurons and designing a program to run on the cluster would be the first step to a biological computer.

Considering that the human brain is basically an advanced form of wetware--not to mention the most powerful processing device still known to man, capable of not only advanced calculations but imaginative thought processes, meaning the ability to design its own complex models and draw conclusions logically (most of the time) advances in wetware are far more than just "cool". Advances in merging biological computing with current technological--hardware--designs could be range from the next step in our evolutionary process, curing memory damaging diseases like Alzheimers or creating the first true artificial intelligence.

The thing is, neurons aren't binary. They have so many connections with other neurons, astrocytes, blood vessels, muscles and the sense organs that they are analog, both in their connections and the response of each connection. And the busier a neuron is, often the more likely it is to stay alive. Unless it gets too busy. I love the work in this PNAS paper, but I think we are closer to AI by our advances in silicon, rather than shoehorning the digital paradigms into a biological system. I think NicoTheUnicorn is more on the right track.

A lot of technology has a "that's cool, but what can you actually do with it?" stage before enough R&D goes into it to reveal practical applications. Electricity comes to mind as an example. It took decades between discovery and home use.

What's the use of being able to do this? Other than to say "that's cool!"

Well, once they make a NAND gate out of this, they can build any kind of gate they want, and presumably they could then build entire wetware ICs. I'm not sure of its real usage, though. Perhaps in equipment that is intended for missions where it will be running continuously, without human intervention, for very long periods of time? A cell's repairability and adaptability might make them useful in situations like that. (Speculating, here.)

What's the use of being able to do this? Other than to say "that's cool!"

Well, once they make a NAND gate out of this, they can build any kind of gate they want, and presumably they could then build entire wetware ICs. I'm not sure of its real usage, though. Perhaps in equipment that is intended for missions where it will be running continuously, without human intervention, for very long periods of time? A cell's repairability and adaptability might make them useful in situations like that. (Speculating, here.)

What's the use of being able to do this? Other than to say "that's cool!"

A working wetware AND gate would be the first step to creating an artificial neuron. Properly setting up a cluster of these neurons and designing a program to run on the cluster would be the first step to a biological computer.

Considering that the human brain is basically an advanced form of wetware--not to mention the most powerful processing device still known to man, capable of not only advanced calculations but imaginative thought processes, meaning the ability to design its own complex models and draw conclusions logically (most of the time) advances in wetware are far more than just "cool". Advances in merging biological computing with current technological--hardware--designs could be range from the next step in our evolutionary process, curing memory damaging diseases like Alzheimers or creating the first true artificial intelligence.

Except a neuron isn't an AND gate. It is most certainly not the first step. Note: brains are not digital

What's the use of being able to do this? Other than to say "that's cool!"

Well, once they make a NAND gate out of this, they can build any kind of gate they want, and presumably they could then build entire wetware ICs. I'm not sure of its real usage, though. Perhaps in equipment that is intended for missions where it will be running continuously, without human intervention, for very long periods of time? A cell's repairability and adaptability might make them useful in situations like that. (Speculating, here.)

One thing to keep in mind, genetic circuits are very very slow, on a good day they take 10s of mins to operate. If you're going to build logic gates it would be better to design gates using just proteins. Plus its not as if this is the first gate that has been build, what is novel is the way they did it.

I only saw how to turn it on in the article; how about turning it off? Does this output only continue so long as we continue supplying those particular sugars? The way the article reads, the sugars trigger the action and then it's self-perpetuating after that (until the cell keels over). It wouldn't seem to be very useful if it's effectively acting as a one-time use switch.